Comparative Genomic Analysis as a Tool in Revealing Gene Features

David L. Baillie
Department of Mol. Biology and Biochem.
Simon Fraser University
8888 University Drive
Burnaby, B.C.
Canada V5A 1S6
telephone: 1-604-268-6590
fax: 1-604-291-5583
email: baillie@sfu.ca
prestype: Platform
presenter: David Baillie

David L. Baillie1, Nigel O'Neil2, Greg Vatcher3, Steve Jones3 and Marco Marra3
1Simon Fraser University, Canada
2Sanger Centre, UK
3B.C. Genome Research Centre, Canada

The Caenorhabditis elegans genome was completed almost two years ago. The sequence is 98 million bases and contains the about 19,000 protein encoding elements. A number of approaches are being taken to reveal the function of each of these coding elements. An international consortium has undertaken the selection of psoralen induced knockouts of all of the coding elements. This is being done in a community driven manner and requests for specific knockouts can be made at http://elegans.bcgsc.bc.ca/knockout.shtml. In addition chips containing arrays of all the putative genes are available for analysis of gene expression at http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html. A large scale EST project with expression information for each cDNA is being done by Yugi Kohara and his data is accessable at http://www.ddbj.nig.ac.jp/htmls/c-elegans/html/CE_INDEX.html. We have been analyzing an area defined by the deficiency sDf125 (about 400,000 BPs) to determine the number of essential genes in this region. We have produced EMS induce lethal alleles of 15 of the 90 genes in the region. Over half of the genes have only one alleles at this time, thus it appears that the number of genes that have essential roles is greater than 30% in this region. We have used a library of overlapping cosmid transgenic containg animals to determine the genes associated with many of our alleles. We have used the sequence of the closely related nematode C. briggsae aid in the determination of the structure of these genes. Examples will be given of the types of information that can be derived from this approach.



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